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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

主页: http://www.biomedcentral.com/bmcsystbiol

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Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design

Brett A Boghigian, Hai Shi, Kyongbum Lee, Blaine A Pfeifer

Robust dynamical pattern formation from a multifunctional minimal genetic circuit

Guillermo Rodrigo, Javier Carrera, Santiago F Elena, Alfonso Jaramillo

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects

Jacqueline M Dresch, Xiaozhou Liu, David N Arnosti, Ahmet Ay

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network

Tatiana Baumuratova, Didier Surdez, Bernard Delyon, Gautier Stoll, Olivier Delattre, Ovidiu Radulescu, Anne Siegel

Combinatorial regulation of transcription factors and microRNAs

Naifang Su, Yufu Wang, Minping Qian, Minghua Deng

Information propagation within the Genetic Network of Saccharomyces cerevisiae

Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne CV Baici, Timothy R Hughes, Olli Yli-Harja, Gordon Chua, Andre S Ribeiro

Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis

Chen Yao, Hongdong Li, Chenggui Zhou, Lin Zhang, Jinfeng Zou, Zheng Guo

Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin

Qiang Zhang, Sudin Bhattacharya, Douglas E Kline, Robert B Crawford, Rory B Conolly, Russell S Thomas, Norbert E Kaminski, Melvin E Andersen

Patterns of human gene expression variance show strong associations with signaling network hierarchy

Kakajan Komurov, Prahlad T Ram

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram

Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano

Integrated cellular network of transcription regulations and protein-protein interactions

Yu-Chao Wang, Bor-Sen Chen

Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

Michael A Dewar, Visakan Kadirkamanathan, Manfred Opper, Guido Sanguinetti

Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro

Bart S Hendriks, Kelly M Seidl, Jeffrey R Chabot

OptFlux: an open-source software platform for in silico metabolic engineering

Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vila？a, Sim？o Soares, José P Pinto, Jens Nielsen, Kiran R Patil, Eugénio C Ferreira, Miguel Rocha

Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP

Dominic P Tolle, Nicolas Le Novère

The internal state of medium spiny neurons varies in response to different input signals

Zhen Qi, Gary W Miller, Eberhard O Voit

The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis

Matteo Brilli, Marco Fondi, Renato Fani, Alessio Mengoni, Lorenzo Ferri, Marco Bazzicalupo, Emanuele G Biondi

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Seth B Roberts, Christopher M Gowen, J Paul Brooks, Stephen S Fong

Prediction of novel synthetic pathways for the production of desired chemicals

Ayoun Cho, Hongseok Yun, Jin Park, Sang Lee, Sunwon Park

The zipper mechanism in phagocytosis: energetic requirements and variability in phagocytic cup shape

Sylvain Tollis, Anna E Dart, George Tzircotis, Robert G Endres

Inferring genetic interactions via a nonlinear model and an optimization algorithm

Chung-Ming Chen, Chih Lee, Cheng-Long Chuang, Chia-Chang Wang, Grace S Shieh

An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis

Yi Zhang, Kim A Hatch, Joanna Bacon, Lorenz Wernisch

Statistical model comparison applied to common network motifs

Núria Domedel-Puig, Iosifina Pournara, Lorenz Wernisch

Discriminating between rival biochemical network models: three approaches to optimal experiment design

Bence Mélykúti, Elias August, Antonis Papachristodoulou, Hana El-Samad

Probability distributed time delays: integrating spatial effects into temporal models

Tatiana T Marquez-Lago, André Leier, Kevin Burrage

Hybrid modeling of biological networks: mixing temporal and qualitative biological properties

Jonathan Fromentin, Damien Eveillard, Olivier Roux

Integration of transcriptional inputs at promoters of the arabinose catabolic pathway

Carla J Davidson, Atul Narang, Michael G Surette

Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer

Tim J Dexter, David Sims, Costas Mitsopoulos, Alan Mackay, Anita Grigoriadis, Amar S Ahmad, Marketa Zvelebil

A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase

Yunfei Li, Ka-sum Lam, Nairanjana Dasgupta, Ping Ye

A plausible mechanism for auxin patterning along the developing root

Victoria V Mironova, Nadezda A Omelyanchuk, Guy Yosiphon, Stanislav I Fadeev, Nikolai A Kolchanov, Eric Mjolsness, Vitaly A Likhoshvai

An information-flow-based model with dissipation, saturation and direction for active pathway inference

Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu, Xiang-Sun Zhang

A quantitative approach to study indirect effects among disease proteins in the human protein interaction network

Thanh-Phuong Nguyen, Ferenc Jordán

Model-based extension of high-throughput to high-content data

Andrea C Pfeifer, Daniel Kaschek, Julie Bachmann, Ursula Klingmüller, Jens Timmer

Simulation methods with extended stability for stiff biochemical Kinetics

Pau Rué, Jordi Villà-Freixa, Kevin Burrage

Identifying essential genes in bacterial metabolic networks with machine learning methods

Kitiporn Plaimas, Roland Eils, Rainer K？nig

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

Sobia Raza, Neil McDerment, Paul A Lacaze, Kevin Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C Freeman

Inferring the physical connectivity of complex networks from their functional dynamics

Hung Ta, Chang Yoon, Liisa Holm, Seung Han

A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior

Mi Zhang, William R Schafer, Rainer Breitling

Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans

Suresh Swain, Jodie F Wren, Stephen R Stürzenbaum, Peter Kille, A John Morgan, Tjalling Jager, Martijs J Jonker, Peter K Hankard, Claus Svendsen, Jenifer Owen, B Ann Hedley, Mark Blaxter, David J Spurgeon

Integrated network analysis of transcriptomic and proteomic data in psoriasis

Eleonora Piruzian, Sergey Bruskin, Alex Ishkin, Rustam Abdeev, Sergey Moshkovskii, Stanislav Melnik, Yuri Nikolsky, Tatiana Nikolskaya

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria

Hidde de Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann

Robustness from flexibility in the fungal circadian clock

Ozgur E Akman, David A Rand, Paul E Brown, Andrew J Millar

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

David van Dijk, Gokhan Ertaylan, Charles AB Boucher, Peter MA Sloot

Optimization strategies for metabolic networks

Alexandre Domingues, Susana Vinga, Jo？o M Lemos

Increased entropy of signal transduction in the cancer metastasis phenotype

Andrew E Teschendorff, Simone Severini

Ultrasensitive Responses and Specificity in Cell Signaling

Seth Haney, Lee Bardwell, Qing Nie

Protein complex prediction based on k-connected subgraphs in protein interaction network

Mahnaz Habibi, Changiz Eslahchi, Limsoon Wong

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

Chen-Ching Lin, Jen-Tsung Hsiang, Chia-Yi Wu, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang

Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

Kaspar Valgepea, Kaarel Adamberg, Ranno Nahku, Petri-Jaan Lahtvee, Liisa Arike, Raivo Vilu

Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron

Marc Jungbluth, Christian Renicke, Christof Taxis

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